Proteomic dynamics in endochondral ossification: insights from antler tip analysis.

Background: The antler primary growth center, located at the distal tip of the growing antler, comprises five consecutive tissue zones beneath the velvet skin. Because the outermost reserve mesenchyme contains blastema progenitor cells with multipotent differentiation capacity, antler regeneration recapitulates embryonic skeletal development through endochondral ossification (ECO). The molecular mechanisms governing cell fate decisions and tissue morphogenesis across these zones remain poorly understood. Methods: We profiled the proteome of the sika deer ( Results: A total of 8,173 proteins were identified across the five tissue zones, representing the most comprehensive proteomic coverage of the antler growth center. Clustering analyses resolved distinct protein expression modules corresponding to sequential ECO stages from mesenchymal proliferation in the reserve mesenchyme to cartilage mineralization in the innermost zone. Deep proteome coverage enabled detection of low-abundance chondrogenic transcription factors SOX9, SOX6, and RUNX3, whose spatial expression matched their known roles in chondrogenesis. At the protein level, the reserve mesenchyme co-expressed 11 embryonic and 23 mesenchymal stem cell markers, indicating that antler stem cells represented a unique mesenchymal stem cell (MSC) population possessing partial embryonic stem cell (ESC)-like features. Conclusions: This study provides a spatially resolved proteomic atlas of the complete antler growth center and identifies key regulatory proteins at each stage of endochondral ossification. The findings offer new insights into progenitor cell characteristics, transcription factor activity, and protein dynamics during bone development, with potential relevance to bone repair and regenerative medicine.